The purpose of this patch is to add a rule for the building of probcons-RNA.

--- probcons.orig/Makefile
+++ probcons/Makefile
@@ -16,6 +16,7 @@
 ################################################################################
 
 OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
 
 # debug mode    
 #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
@@ -25,13 +26,16 @@
 
 # release mode
 #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
+
 CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
+
 
 ################################################################################
 # 3) Dependencies
 ################################################################################
 
-TARGETS = probcons compare project makegnuplot
+TARGETS = probcons probcons-RNA compare project makegnuplot
 
 .PHONY : all
 all : $(TARGETS)
@@ -42,6 +46,9 @@
 compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
 	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
 
+probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
+
 fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
 
